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MartinBeal authored and cran-robot committed Oct 10, 2022
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8 changes: 4 additions & 4 deletions DESCRIPTION
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Package: track2KBA
Title: Identifying Important Areas from Animal Tracking Data
Version: 1.0.2
Version: 1.0.3
Authors@R: c(
person("Martin", "Beal", email = "martinbeal88@gmail.com", role = c("aut","cre"), comment = c(ORCID = "0000-0003-1654-1410")),
person("Steffen", "Oppel", email = "steffen.oppel@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-1654-1410")),
Expand All @@ -22,7 +22,7 @@ Depends: R (>= 2.10)
License: LGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
RoxygenNote: 7.2.0
BugReports: https://github.com/BirdLifeInternational/track2kba/issues
Suggests: adehabitatLT, doParallel, knitr, parallel, rmarkdown,
tinytest
Expand All @@ -32,7 +32,7 @@ Imports: adehabitatHR, dplyr, foreach, geosphere, ggplot2, lubridate,
raster, rgdal (>= 1.5-0), rgeos, rlang, sf (>= 0.7-4), sp (>=
1.4-1), tidyr
NeedsCompilation: no
Packaged: 2022-04-26 14:58:38 UTC; Martim Bill
Packaged: 2022-10-06 10:59:50 UTC; Martim Bill
Author: Martin Beal [aut, cre] (<https://orcid.org/0000-0003-1654-1410>),
Steffen Oppel [aut] (<https://orcid.org/0000-0003-1654-1410>),
Maria Dias [aut] (<https://orcid.org/0000-0002-7281-4391>),
Expand All @@ -44,4 +44,4 @@ Author: Martin Beal [aut, cre] (<https://orcid.org/0000-0003-1654-1410>),
Ben Lascelles [ctb]
Maintainer: Martin Beal <martinbeal88@gmail.com>
Repository: CRAN
Date/Publication: 2022-04-26 16:00:02 UTC
Date/Publication: 2022-10-10 18:50:02 UTC
60 changes: 30 additions & 30 deletions MD5
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18e4bbaf9b46e65fecc7473861e4f7bb *DESCRIPTION
22607042fb045b763fd0ee447d27bd28 *DESCRIPTION
93e3b9916b77a848ae93ebc3c11542bd *NAMESPACE
83e568f7597ce837e83b2d83dc87eb4e *NEWS.md
13c3503e59ce7e4c6b7926e22fe8d278 *NEWS.md
5afb06434961b0be419fbe9735f7b859 *R/data.R
6103697a1209ac99d60ebf5e8443cfb0 *R/estSpaceUse.r
ec39b7061af0d398a8c72e55933e8a43 *R/findScale.R
9cbbab4621c0519c8cadd29966630a25 *R/estSpaceUse.r
c7fb7f51684f13906193063f7b60fba2 *R/findScale.R
9b572462a47ddcf629dcefc35a23f337 *R/findSite.R
634f7dfde76b4a888af6058b5787ea46 *R/formatFields.R
f02218e46dce91e91031424a90ba5730 *R/indEffectTest.R
ab8463d85fd6da48fe7dcf472b9c3936 *R/mapKDE.R
cea8ef0eca382be9be924b9e981c307c *R/mapKDE.R
4c5697fee9ec3f9fe8ef63b982d6ef7e *R/mapSite.R
df17739628efa1556aeb7870d9f3b08d *R/mapTrips.R
7fea76ab1d809a59775d86ef93da0fc5 *R/move2KBA.r
c7bfad1743d262db2f2754ae3e6468a5 *R/projectTracks.R
901d68fb8e9a1ef9ce3ee1ce8cce58ab *R/projectTracks.R
02cd2377fe5221bfc8978e1d12273f27 *R/repAssess.r
05e2ee19cab1a56b2c136d5376a3bee5 *R/tripSplit.r
39c6d854a52914f0d575f9bdff5b3074 *R/tripSummary.r
c0c01deda993b653a950260bfc824ec9 *README.md
b5ce74432b1e2cfb81bd9e24075ebcb4 *build/vignette.rds
0e7c3fc8ec04b94c7c9167c25342e562 *R/tripSplit.r
8cf47c186c3705ff92c3d2e81daf4954 *R/tripSummary.r
22befc0d38547c0aea71ecc066d6d8fb *README.md
afdd9cbb1410d4dbd426d5fbdfb41a40 *build/vignette.rds
0ec0d3e2720c25cf1f2928f2c4771bbc *data/KDE_example.rda
6aa6e7e87ffbef6b951ff18d494cd295 *data/boobies.rda
31384b8205170d4954fb5c09392d600f *inst/CITATION
89ee74ee7a77e77fa2245026eb15b91c *inst/doc/track2kba_workflow.R
aa690e44704a2fb3c36a3dce4d88730b *inst/doc/track2kba_workflow.Rmd
92ba28cf12e7e1d69307391b7a8871ce *inst/doc/track2kba_workflow.html
73fe4d89e2bc1053dea10c14a4fe950a *inst/doc/track2kba_workflow.Rmd
937ce602499ff5cd0a7a9639643a1e5b *inst/doc/track2kba_workflow.html
6456da43b40fbc0072f215c4c59dd47f *inst/tinytest/boobies_testdata.csv
3a641a98f789ced53371662e8fb83095 *inst/tinytest/movebank_testdata.csv
b372cfe93ecfed0c206c9b2c97bd88b1 *inst/tinytest/test_estSpaceUse.R
526b0dff9022c90bc09b0273d25de813 *inst/tinytest/test_findScale.R
5ddf15433e1993bff132f4c60cbb6acb *inst/tinytest/test_findSite.R
9b20f65b96509362dd3cfe80142db4c5 *inst/tinytest/test_formatFields.R
50b4fb6e8fea1de6b3c8d0779eb3f15b *inst/tinytest/test_indEffectTest.R
6f0c4c87a43499de0f6ead939814a0e5 *inst/tinytest/test_mapKDE.R
d2bcc0b64b8d9ff812e5cc5cc0409a68 *inst/tinytest/test_mapSite.R
45f0f41b5ec68e7285f6c93d6c4f0570 *inst/tinytest/test_mapTrips.R
369fe463e96c36912919563cf7ea531e *inst/tinytest/test_estSpaceUse.R
6662bbae282866095fe81e4b8b0de1cf *inst/tinytest/test_findScale.R
f3ace56926d576ee9e22330b05c06128 *inst/tinytest/test_findSite.R
daf634ebdeb0afbadb314ae700c31ab8 *inst/tinytest/test_formatFields.R
48eaa7a9c5dd58a53c09d8a7676a6629 *inst/tinytest/test_indEffectTest.R
ac7bd33e653a506d1ccc7ac6c26e9ef1 *inst/tinytest/test_mapKDE.R
6169c29531ad2065ea851945b1821b10 *inst/tinytest/test_mapSite.R
7473b0ddfa5c7c85f9fea26b7abfcf69 *inst/tinytest/test_mapTrips.R
c2dea4214f2f56f4cef7f55cd0b0099f *inst/tinytest/test_move2KBA.R
7e616d12d8bdd9576cb13d45899589db *inst/tinytest/test_projectTracks.R
729a5dfeceb742e66eea7667332bd82a *inst/tinytest/test_repAssess.R
5e073ad0c7043ca4df71a5d7bc31c04f *inst/tinytest/test_tripSplit.R
50994fd3d2fd870b35ab4bb47c7b7c71 *inst/tinytest/test_tripSummary.R
6b68206898903f544e897a2f612ed7d3 *inst/tinytest/test_projectTracks.R
bce1f937549a5392fadb9cb81510f1e4 *inst/tinytest/test_repAssess.R
9c9a9994296b5488c70782dc9e5ec7ff *inst/tinytest/test_tripSplit.R
ad21930ed5c2294441fdc5cfe5e13d94 *inst/tinytest/test_tripSummary.R
6901a8f3a46cff4f1598be3fea816edc *man/KDE_example.Rd
94026775a733d058d17d20f788cc52a1 *man/boobies.Rd
c0e9741aa986d789d90538626267ae51 *man/estSpaceUse.Rd
9a1d9790dd10b32fd309c471972b80d0 *man/estSpaceUse.Rd
c2d3fd4403b3fd2888df52181ff194db *man/figures/KBA_sp_plot.png
ec999a2da8b41eb76aedaafba10fee5c *man/figures/estSpaceUse-1.png
c44395cf03534ac7a36d15954ca1f96b *man/figures/findScale-1.png
52df063d44f5bca0f54ff3211953ce11 *man/figures/logo.png
5eaaa0d51bca3db52c7a69117bd21f55 *man/figures/plot_KBA_sf.png
bf7a5d90d020baf91712aba59960d8f8 *man/figures/repAssess-1.png
96c8090440db043fc6ec40e557b19e69 *man/figures/tripSplit-chunk-3-1.png
b454598cf37e2eada7bd9d3da1920220 *man/findScale.Rd
e0b380396639ffe11ecd6c6b73ddb2ae *man/findScale.Rd
c51a0dee672082acef6d752f3797b77d *man/findSite.Rd
bd34091a71c6da3da369a49d264535c2 *man/formatFields.Rd
c144bb694e1693f4641dd5355cd1e593 *man/indEffectTest.Rd
b7347953469348e572ec48fdca79d171 *man/mapKDE.Rd
e5c66ef6047c99b737a9d968d0173899 *man/mapKDE.Rd
7821abc97cc970fd04b5964408574dc5 *man/mapSite.Rd
dcc9da9d8d4d9f974a9d623a6229c3d2 *man/mapTrips.Rd
946dd91281defa2ee7e3b6ae8afc646d *man/move2KBA.Rd
c5b88117c9715447561b70e221a0a70c *man/projectTracks.Rd
de5ea416236dc3b57924b9a2d7d247fb *man/repAssess.Rd
71fe2c5d7973bbb7f5f94a3f5c934667 *man/tripSplit.Rd
0e102f9ca9b249f39c811a66f026d62b *man/tripSummary.Rd
c8284681bda7451598fa1a216a7e9106 *man/tripSplit.Rd
e8607639f8fc46495d3efcc1baeae01c *man/tripSummary.Rd
6c302f002a6474c927f8e9c6d051b640 *tests/tinytest.R
c2d3fd4403b3fd2888df52181ff194db *vignettes/KBA_sp_plot.png
ec999a2da8b41eb76aedaafba10fee5c *vignettes/estSpaceUse-1.png
c44395cf03534ac7a36d15954ca1f96b *vignettes/findScale-1.png
5eaaa0d51bca3db52c7a69117bd21f55 *vignettes/plot_KBA_sf.png
bf7a5d90d020baf91712aba59960d8f8 *vignettes/repAssess-1.png
aa690e44704a2fb3c36a3dce4d88730b *vignettes/track2kba_workflow.Rmd
73fe4d89e2bc1053dea10c14a4fe950a *vignettes/track2kba_workflow.Rmd
96c8090440db043fc6ec40e557b19e69 *vignettes/tripSplit-chunk-3-1.png
7 changes: 4 additions & 3 deletions NEWS.md
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# Version 1.0.3
Fixing CRAN checks.
# Version 1.0.2

# Version 1.0.1.9000

# Version 1.0.1

Fixing CRAN checks.
Added 'KDE_example' data file

# Version 1.0.0

First release.
4 changes: 3 additions & 1 deletion R/estSpaceUse.r
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Expand Up @@ -53,11 +53,13 @@
#' \code{\link{findScale}}
#'
#' @examples
#' library(rgdal)
#' library(sp)
#' ## make some play data
#'dataGroup <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1.03, 1),
#' Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1.01, 1),
#' ID = rep("A", 7),
#' DateTime = as.character(
#' DateTime = format(
#' lubridate::ymd_hms("2021-01-01 00:00:00") +
#' lubridate::hours(0:6)
#' )
Expand Down
2 changes: 1 addition & 1 deletion R/findScale.R
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Expand Up @@ -99,7 +99,7 @@
#' dataGroup <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1),
#' Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1),
#' ID = rep("A", 6),
#' DateTime = as.character(
#' DateTime = format(
#' lubridate::ymd_hms("2021-01-01 00:00:00") +
#' lubridate::hours(0:5)
#' )
Expand Down
2 changes: 1 addition & 1 deletion R/mapKDE.R
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Expand Up @@ -27,7 +27,7 @@
#'dataGroup <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1.03, 1),
#' Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1.01, 1),
#' ID = rep("A", 7),
#' DateTime = as.character(
#' DateTime = format(
#' lubridate::ymd_hms("2021-01-01 00:00:00") +
#' lubridate::hours(0:6)
#' )
Expand Down
2 changes: 1 addition & 1 deletion R/projectTracks.R
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Expand Up @@ -119,7 +119,7 @@ projectTracks <- function(dataGroup, projType, custom) {
}
}

if (class(dataGroup) != "SpatialPointsDataFrame") {
if (!"SpatialPointsDataFrame" %in% class(dataGroup)) {

### PREVENT PROJECTION PROBLEMS FOR DATA SPANNING DATELINE ----------------
if (min(dataGroup$Longitude) < -170 & max(dataGroup$Longitude) > 170) {
Expand Down
2 changes: 1 addition & 1 deletion R/tripSplit.r
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Expand Up @@ -56,7 +56,7 @@
#' dataGroup <- data.frame(Longitude = rep(c(1:10, 10:1), 2),
#' Latitude = rep(c(1:10, 10:1), 2),
#' ID = c(rep("A", 20), rep("B", 20)),
#' DateTime = as.character(
#' DateTime = format(
#' lubridate::ymd_hms("2021-01-01 00:00:00") +
#' lubridate::hours(0:19))
#' )
Expand Down
2 changes: 1 addition & 1 deletion R/tripSummary.r
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Expand Up @@ -41,7 +41,7 @@
#' dataGroup <- data.frame(Longitude = rep(c(1:10, 10:1), 2),
#' Latitude = rep(c(1:10, 10:1), 2),
#' ID = c(rep("A", 20), rep("B", 20)),
#' DateTime = as.character(
#' DateTime = format(
#' lubridate::ymd_hms("2021-01-01 00:00:00") +
#' lubridate::hours(0:19))
#' )
Expand Down
4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -109,6 +109,7 @@ when the animals were not on trips. The results of `tripSplit` can be
plotted using `mapTrips` to see some examples of trips.

``` r

str(dataGroup)

trips <- tripSplit(
Expand Down Expand Up @@ -345,6 +346,7 @@ output is independent of the representativness-based importance
threshold.

``` r

mapSite(Site, colony = colony)
```

Expand All @@ -365,7 +367,7 @@ Carneiro, A. P. B., Davies, T. E., Phillips, R. A., Taylor, P. R.,
Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla,
A., Staniland, I., Boyd, C., Catry, P., & Dias, M. P. (2021). track2KBA:
An R package for identifying important sites for biodiversity from
tracking data. Methods in Ecology and Evolution, n/a(n/a).
tracking data. Methods in Ecology and Evolution, 12(12), 2372-2378.
<https://doi.org/10.1111/2041-210X.13713>

### Example data reference
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Binary file modified build/vignette.rds
Binary file not shown.
2 changes: 1 addition & 1 deletion inst/doc/track2kba_workflow.Rmd
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Expand Up @@ -252,7 +252,7 @@ This plot shows the minimum estimated number of birds using the space around the
### Reference
If you use any functions in this package for your work, please use the following citation:

Beal, M., Oppel, S., Handley, J., Pearmain, E. J., Morera-Pujol, V., Carneiro, A. P. B., Davies, T. E., Phillips, R. A., Taylor, P. R., Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla, A., Staniland, I., Boyd, C., Catry, P., & Dias, M. P. (2021). track2KBA: An R package for identifying important sites for biodiversity from tracking data. Methods in Ecology and Evolution, n/a(n/a). https://doi.org/10.1111/2041-210X.13713
Beal, M., Oppel, S., Handley, J., Pearmain, E. J., Morera-Pujol, V., Carneiro, A. P. B., Davies, T. E., Phillips, R. A., Taylor, P. R., Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla, A., Staniland, I., Boyd, C., Catry, P., & Dias, M. P. (2021). track2KBA: An R package for identifying important sites for biodiversity from tracking data. Methods in Ecology and Evolution, 12(12), 2372-2378. https://doi.org/10.1111/2041-210X.13713

### Example data
Oppel, S., Beard, A., Fox, D., Mackley, E., Leat, E., Henry, L., Clingham, E., Fowler, N., Sim, J., Sommerfeld, J., Weber, N., Weber, S., Bolton, M., 2015. *Foraging distribution of a tropical seabird supports Ashmole’s hypothesis of population regulation. Behav Ecol Sociobiol 69, 915–926. https://doi.org/10.1007/s00265-015-1903-3*
Expand Down
3 changes: 2 additions & 1 deletion inst/doc/track2kba_workflow.html
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Expand Up @@ -617,7 +617,8 @@ <h3>Reference</h3>
Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla,
A., Staniland, I., Boyd, C., Catry, P., &amp; Dias, M. P. (2021).
track2KBA: An R package for identifying important sites for biodiversity
from tracking data. Methods in Ecology and Evolution, n/a(n/a). <a href="https://doi.org/10.1111/2041-210X.13713" class="uri">https://doi.org/10.1111/2041-210X.13713</a></p>
from tracking data. Methods in Ecology and Evolution, 12(12), 2372-2378.
<a href="https://doi.org/10.1111/2041-210X.13713" class="uri">https://doi.org/10.1111/2041-210X.13713</a></p>
</div>
<div id="example-data" class="section level3">
<h3>Example data</h3>
Expand Down
2 changes: 2 additions & 0 deletions inst/tinytest/test_estSpaceUse.R
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@@ -1,5 +1,7 @@
library(track2KBA)
library(lubridate)
library(rgdal)
library(sp)

dat <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1.03, 1),
Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1.01, 1),
Expand Down
5 changes: 3 additions & 2 deletions inst/tinytest/test_findScale.R
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Expand Up @@ -2,11 +2,12 @@ library(track2KBA)
library(lubridate)
library(sp)
library(dplyr)
library(rgdal)

dat <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1),
Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1),
ID = rep("A", 6),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:5))
)

Expand Down Expand Up @@ -69,7 +70,7 @@ expect_true(findScale(trips2)$step_length == findScale(trips)$step_length,
dat <- data.frame(Longitude = c(1, 1.1, 2, 2.1, 1.5, 1),
Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1),
ID = rep("A", 6),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:5))
)

Expand Down
2 changes: 2 additions & 0 deletions inst/tinytest/test_findSite.R
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@@ -1,4 +1,6 @@
library(track2KBA)
library(rgdal)
library(sp)

dat <- read.csv("boobies_testdata.csv")
trips <- projectTracks(dat, projType = "azim", custom = TRUE)
Expand Down
4 changes: 2 additions & 2 deletions inst/tinytest/test_formatFields.R
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ library(lubridate)

dat <- data.frame(x = rep(1:10, 2), y = rep(1:10, 2),
id = c(rep("A", 10), rep("B", 10)),
dt = as.character(ymd_hms("2021-01-01 00:00:00") + hours(0:9))
dt = format(ymd_hms("2021-01-01 00:00:00") + hours(0:9))
)

expect_error(formatFields("dat"), pattern = "Object")
Expand Down Expand Up @@ -106,7 +106,7 @@ expect_true( "ID" %in% colnames(formatFields(dat2,
## separate date and time columns
dat2 <- data.frame(x = rep(1:10, 2), y = rep(1:10, 2),
id = c(rep("A", 10), rep("B", 10)),
dt = as.character(ymd_hms("2021-01-01 00:00:00") + hours(0:9))
dt = format(ymd_hms("2021-01-01 00:00:00") + hours(0:9))
)

dat2$date <- do.call(rbind, strsplit(dat2$dt, split=" ", fixed=TRUE))[,1]
Expand Down
4 changes: 3 additions & 1 deletion inst/tinytest/test_indEffectTest.R
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@@ -1,12 +1,14 @@
library(track2KBA)
library(lubridate)
library(rgdal)
library(sp)

dat <- data.frame(Longitude = rep(c(seq(1, 1.1, length.out=10),
seq(1.2, 1, length.out=10)), 2),
Latitude = rep(c(seq(1, 1.1, length.out=10),
seq(1.2, 1, length.out=10)), 2),
ID = c(rep("A", 40)),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:39))
)

Expand Down
4 changes: 3 additions & 1 deletion inst/tinytest/test_mapKDE.R
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
library(track2KBA)
library(lubridate)
library(rgdal)
library(sp)

dat <- data.frame(Longitude = c(1, 1.01, 1.02, 1.04, 1.05, 1.03, 1),
Latitude = c(1, 1.01, 1.02, 1.03, 1.021, 1.01, 1),
ID = rep("A", 7),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:6))
)
colony <- data.frame(Longitude = dat$Longitude[1], Latitude = dat$Latitude[1])
Expand Down
2 changes: 2 additions & 0 deletions inst/tinytest/test_mapSite.R
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@@ -1,4 +1,6 @@
library(track2KBA)
library(rgdal)
library(sp)

dat <- read.csv("boobies_testdata.csv")
colony <- data.frame(Longitude = dat$Longitude[1], Latitude = dat$Latitude[1])
Expand Down
7 changes: 5 additions & 2 deletions inst/tinytest/test_mapTrips.R
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@@ -1,9 +1,12 @@
library(track2KBA)
library(lubridate)
library(rgdal)
library(sp)

dat <- data.frame(Longitude = rep(c(1:10, 10:1), 2),
Latitude = rep(c(1:10, 10:1), 2),
ID = c(rep("A", 20), rep("B", 20)),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:19))
)

Expand All @@ -24,7 +27,7 @@ expect_silent(mapTrips(trips, colony, IDs = 1))
dat_idl <- data.frame(Longitude = rep(c(-170:-179, 179:170)),
Latitude = rep(c(1:10, 10:1)),
ID = c(rep("A", 20)),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:19))
)

Expand Down
6 changes: 4 additions & 2 deletions inst/tinytest/test_projectTracks.R
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
library(track2KBA)
library(lubridate)
library(rgdal)
library(sp)

dat <- data.frame(Longitude = c(1, 2, 3, 1),
Latitude = c(1, 1, 2, 1),
ID = rep("A", 4),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:3))
)

Expand Down Expand Up @@ -44,7 +46,7 @@ expect_error(projectTracks(dataGroup = dat_prj,
dat_idl <- data.frame(Longitude = rep(c(-170:-179, 179:170)),
Latitude = rep(c(1:10, 10:1)),
ID = c(rep("A", 20)),
DateTime = as.character(
DateTime = format(
ymd_hms("2021-01-01 00:00:00") + hours(0:19))
)

Expand Down

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